Datasets:
vgainullin
/
xciting_data

Dataset card Data Studio Files
xet
 Community
1
paragraph_index
int64
sec
string
p_has_citation
int64
cites
string
citeids
list
pmid
int64
cited_id
string
sentences
string
all_sent_cites
list
sent_len
int64
sentence_batch_index
int64
sent_has_citation
float64
qc_fail
bool
cited_sentence
string
cites_in_sentence
list
cln_sentence
string
is_cap
bool
is_alpha
bool
ends_wp
bool
cit_qc
bool
lgtm
bool
__index_level_0__
int64
0
DISCUSSION
1
6
[ "b6", "b25", "b26", "b21", "b22", "b27" ]
16,845,117
NA|pmid-15576025|pmid-15854658|pmid-16424331|pmid-12112693|pmid-15215455|pmid-15215355|pmid-15215444|pmid-15215359|pmid-15215453|pmid-15980464|pmid-15576025|pmid-11161105|pmid-8844870|pmid-12691985|pmid-15229884|pmid-9796821
The main limitation of OPAAS, at its current version, arose from a compromise to trade for computational efficiency, which dictates that a structure must possess at least three SSEs to be compared (21,22); elimination of this limitation is in progress.
[ "6", "25", "26", "21", "22", "27" ]
252
6,300
0
false
The main limitation of OPAAS, at its current version, arose from a compromise to trade for computational efficiency, which dictates that a structure must possess at least three SSEs to be compared ; elimination of this limitation is in progress.
[ "21,22" ]
The main limitation of OPAAS, at its current version, arose from a compromise to trade for computational efficiency, which dictates that a structure must possess at least three SSEs to be compared ; elimination of this limitation is in progress.
true
true
true
true
true
1,035
0
DISCUSSION
1
27
[ "b6", "b25", "b26", "b21", "b22", "b27" ]
16,845,117
NA|pmid-15576025|pmid-15854658|pmid-16424331|pmid-12112693|pmid-15215455|pmid-15215355|pmid-15215444|pmid-15215359|pmid-15215453|pmid-15980464|pmid-15576025|pmid-11161105|pmid-8844870|pmid-12691985|pmid-15229884|pmid-9796821
Significantly, our server allows database search with an efficiency comparable that of the popular CE server (27), despite ours being run on a personal computer (Pentium IV) and being asked to find alternative alignments.
[ "6", "25", "26", "21", "22", "27" ]
221
6,301
1
false
Significantly, our server allows database search with an efficiency comparable that of the popular CE server, despite ours being run on a personal computer (Pentium IV) and being asked to find alternative alignments.
[ "27" ]
Significantly, our server allows database search with an efficiency comparable that of the popular CE server, despite ours being run on a personal computer (Pentium IV) and being asked to find alternative alignments.
true
true
true
true
true
1,035
0
DISCUSSION
1
6
[ "b6", "b25", "b26", "b21", "b22", "b27" ]
16,845,117
NA|pmid-15576025|pmid-15854658|pmid-16424331|pmid-12112693|pmid-15215455|pmid-15215355|pmid-15215444|pmid-15215359|pmid-15215453|pmid-15980464|pmid-15576025|pmid-11161105|pmid-8844870|pmid-12691985|pmid-15229884|pmid-9796821
The source code of OPAAS is also available at the server for free download for standalone computations and for incorporation of structure database other than SCOP.
[ "6", "25", "26", "21", "22", "27" ]
163
6,302
0
false
The source code of OPAAS is also available at the server for free download for standalone computations and for incorporation of structure database other than SCOP.
[]
The source code of OPAAS is also available at the server for free download for standalone computations and for incorporation of structure database other than SCOP.
true
true
true
true
true
1,035
0
INTRODUCTION
1
1–4
[ "B1 B2 B3 B4", "B1 B2 B3", "B5" ]
17,617,643
pmid-9084180|pmid-9401028|pmid-9045819|pmid-14973026|pmid-9084180|pmid-9401028|pmid-9045819|pmid-9620981
The transcription factor AraR controls the utilization of carbohydrates in Bacillus subtilis.
[ "1–4", "1–3", "5" ]
93
6,303
0
false
The transcription factor AraR controls the utilization of carbohydrates in Bacillus subtilis.
[]
The transcription factor AraR controls the utilization of carbohydrates in Bacillus subtilis.
true
true
true
true
true
1,036
0
INTRODUCTION
1
1–4
[ "B1 B2 B3 B4", "B1 B2 B3", "B5" ]
17,617,643
pmid-9084180|pmid-9401028|pmid-9045819|pmid-14973026|pmid-9084180|pmid-9401028|pmid-9045819|pmid-9620981
The control exerted by AraR is modulated by the presence of the effector molecule arabinose leading to induction of expression of at least 13 genes, comprising the arabinose (ara) regulon, which includes the araR gene (1–4).
[ "1–4", "1–3", "5" ]
224
6,304
1
false
The control exerted by AraR is modulated by the presence of the effector molecule arabinose leading to induction of expression of at least 13 genes, comprising the arabinose (ara) regulon, which includes the araR gene.
[ "1–4" ]
The control exerted by AraR is modulated by the presence of the effector molecule arabinose leading to induction of expression of at least 13 genes, comprising the arabinose (ara) regulon, which includes the araR gene.
true
true
true
true
true
1,036
0
INTRODUCTION
1
1–4
[ "B1 B2 B3 B4", "B1 B2 B3", "B5" ]
17,617,643
pmid-9084180|pmid-9401028|pmid-9045819|pmid-14973026|pmid-9084180|pmid-9401028|pmid-9045819|pmid-9620981
The products of these genes (araABDLMNPQ-abfA, araE, abnA and xsa) include extracellular and intracellular catabolic enzymes involved in the degradation of arabinose, galactose and xylose containing polysaccharides, uptake of these sugars into the cell and further catabolism of l-arabinose and arabinose oligomers (1–3,...
[ "1–4", "1–3", "5" ]
323
6,305
0
false
The products of these genes (araABDLMNPQ-abfA, araE, abnA and xsa) include extracellular and intracellular catabolic enzymes involved in the degradation of arabinose, galactose and xylose containing polysaccharides, uptake of these sugars into the cell and further catabolism of l-arabinose and arabinose oligomers.
[ "1–3,5" ]
The products of these genes (araABDLMNPQ-abfA, araE, abnA and xsa) include extracellular and intracellular catabolic enzymes involved in the degradation of arabinose, galactose and xylose containing polysaccharides, uptake of these sugars into the cell and further catabolism of l-arabinose and arabinose oligomers.
true
true
true
true
true
1,036
1
INTRODUCTION
1
4
[ "B4", "B6", "B7", "B4", "B6", "B7" ]
17,617,643
pmid-14973026|pmid-10417639|pmid-11418559|pmid-14973026|pmid-10417639|pmid-11418559
A key property of AraR is its ability to bind specific DNA sequences in the absence of the inducer l-arabinose, as determined by DNAse I footprinting analysis (4,6,7).
[ "4", "6", "7", "4", "6", "7" ]
167
6,306
0
false
A key property of AraR is its ability to bind specific DNA sequences in the absence of the inducer l-arabinose, as determined by DNAse I footprinting analysis.
[ "4,6,7" ]
A key property of AraR is its ability to bind specific DNA sequences in the absence of the inducer l-arabinose, as determined by DNAse I footprinting analysis.
true
true
true
true
true
1,037
1
INTRODUCTION
1
4
[ "B4", "B6", "B7", "B4", "B6", "B7" ]
17,617,643
pmid-14973026|pmid-10417639|pmid-11418559|pmid-14973026|pmid-10417639|pmid-11418559
AraR recognizes and binds at least eight palindromic operator sequences, located in the five known arabinose-inducible promoters.
[ "4", "6", "7", "4", "6", "7" ]
129
6,307
0
false
AraR recognizes and binds at least eight palindromic operator sequences, located in the five known arabinose-inducible promoters.
[]
AraR recognizes and binds at least eight palindromic operator sequences, located in the five known arabinose-inducible promoters.
true
true
true
true
true
1,037
1
INTRODUCTION
1
4
[ "B4", "B6", "B7", "B4", "B6", "B7" ]
17,617,643
pmid-14973026|pmid-10417639|pmid-11418559|pmid-14973026|pmid-10417639|pmid-11418559
Three of these promoters contain two ara boxes: the promoter of the araABDLMNPQ-abfA operon (boxes ORA1 and ORA2), of araE (ORE1 and ORE2) and of xsa (ORX1 and ORX2).
[ "4", "6", "7", "4", "6", "7" ]
166
6,308
0
false
Three of these promoters contain two ara boxes: the promoter of the araABDLMNPQ-abfA operon (boxes ORA1 and ORA2), of araE (ORE1 and ORE2) and of xsa (ORX1 and ORX2).
[]
Three of these promoters contain two ara boxes: the promoter of the araABDLMNPQ-abfA operon (boxes ORA1 and ORA2), of araE (ORE1 and ORE2) and of xsa (ORX1 and ORX2).
true
true
true
true
true
1,037
1
INTRODUCTION
1
4
[ "B4", "B6", "B7", "B4", "B6", "B7" ]
17,617,643
pmid-14973026|pmid-10417639|pmid-11418559|pmid-14973026|pmid-10417639|pmid-11418559
In the cases of the genes araR and abnA, a single ara box is present (ORR3 and ORB1).
[ "4", "6", "7", "4", "6", "7" ]
85
6,309
0
false
In the cases of the genes araR and abnA, a single ara box is present (ORR3 and ORB1).
[]
In the cases of the genes araR and abnA, a single ara box is present (ORR3 and ORB1).
true
true
true
true
true
1,037
1
INTRODUCTION
1
4
[ "B4", "B6", "B7", "B4", "B6", "B7" ]
17,617,643
pmid-14973026|pmid-10417639|pmid-11418559|pmid-14973026|pmid-10417639|pmid-11418559
AraR binding to the promoters displaying two ara boxes is cooperative, requiring in phase and properly spaced operators, and involves the formation of a small loop in the DNA.
[ "4", "6", "7", "4", "6", "7" ]
175
6,310
0
false
AraR binding to the promoters displaying two ara boxes is cooperative, requiring in phase and properly spaced operators, and involves the formation of a small loop in the DNA.
[]
AraR binding to the promoters displaying two ara boxes is cooperative, requiring in phase and properly spaced operators, and involves the formation of a small loop in the DNA.
true
true
true
true
true
1,037
1
INTRODUCTION
1
4
[ "B4", "B6", "B7", "B4", "B6", "B7" ]
17,617,643
pmid-14973026|pmid-10417639|pmid-11418559|pmid-14973026|pmid-10417639|pmid-11418559
These two mechanistically diverse modes of action of AraR result in distinct levels of transcriptional regulation, as cooperative binding to two ara boxes results in a high level of repression while interaction with a single operator allows a more flexible control (4,6,7).
[ "4", "6", "7", "4", "6", "7" ]
273
6,311
0
false
These two mechanistically diverse modes of action of AraR result in distinct levels of transcriptional regulation, as cooperative binding to two ara boxes results in a high level of repression while interaction with a single operator allows a more flexible control.
[ "4,6,7" ]
These two mechanistically diverse modes of action of AraR result in distinct levels of transcriptional regulation, as cooperative binding to two ara boxes results in a high level of repression while interaction with a single operator allows a more flexible control.
true
true
true
true
true
1,037
2
INTRODUCTION
1
9
[ "B1", "B6", "B8", "B9", "B10", "B11", "B12", "B13" ]
17,617,643
pmid-9084180|pmid-10417639|pmid-16585763|pmid-2060763|pmid-1639817|pmid-11756427|pmid-12867439|pmid-12368255
AraR is a 362 amino acid homodimeric protein that shows a chimeric organization, consisting of two functional domains with different phylogenetic origins (1,6,8): a small N-terminal DNA-binding domain (DBD) comprising a winged helix–turn–helix (HTH) motif belonging to the GntR family of transcriptional regulators (9) a...
[ "1", "6", "8", "9", "10", "11", "12", "13" ]
449
6,312
1
false
AraR is a 362 amino acid homodimeric protein that shows a chimeric organization, consisting of two functional domains with different phylogenetic origins : a small N-terminal DNA-binding domain (DBD) comprising a winged helix–turn–helix (HTH) motif belonging to the GntR family of transcriptional regulators and a larger...
[ "1,6,8", "9", "10" ]
AraR is a 362 amino acid homodimeric protein that shows a chimeric organization, consisting of two functional domains with different phylogenetic origins : a small N-terminal DNA-binding domain (DBD) comprising a winged helix–turn–helix (HTH) motif belonging to the GntR family of transcriptional regulators and a larger...
true
true
true
true
true
1,038
2
INTRODUCTION
1
1
[ "B1", "B6", "B8", "B9", "B10", "B11", "B12", "B13" ]
17,617,643
pmid-9084180|pmid-10417639|pmid-16585763|pmid-2060763|pmid-1639817|pmid-11756427|pmid-12867439|pmid-12368255
AraR typifies one of the six GntR-subfamilies of proteins (11,12).
[ "1", "6", "8", "9", "10", "11", "12", "13" ]
66
6,313
0
false
AraR typifies one of the six GntR-subfamilies of proteins.
[ "11,12" ]
AraR typifies one of the six GntR-subfamilies of proteins.
true
true
true
true
true
1,038
2
INTRODUCTION
1
1
[ "B1", "B6", "B8", "B9", "B10", "B11", "B12", "B13" ]
17,617,643
pmid-9084180|pmid-10417639|pmid-16585763|pmid-2060763|pmid-1639817|pmid-11756427|pmid-12867439|pmid-12368255
Currently, there are 54 members of this rapidly growing class of proteins, which can be found in prokaryotes [CDART database; (13)].
[ "1", "6", "8", "9", "10", "11", "12", "13" ]
132
6,314
0
false
Currently, there are 54 members of this rapidly growing class of proteins, which can be found in prokaryotes.
[ "CDART database; (13)" ]
Currently, there are 54 members of this rapidly growing class of proteins, which can be found in prokaryotes.
true
true
true
true
true
1,038
3
INTRODUCTION
1
8
[ "B8", "B8" ]
17,617,643
pmid-16585763|pmid-16585763
Previously, a model for AraR was derived using comparative modelling based on crystal structures of FadR (DBD) and PurR (COOH domain) from Escherichia coli (8).
[ "8", "8" ]
160
6,315
1
false
Previously, a model for AraR was derived using comparative modelling based on crystal structures of FadR (DBD) and PurR (COOH domain) from Escherichia coli.
[ "8" ]
Previously, a model for AraR was derived using comparative modelling based on crystal structures of FadR (DBD) and PurR (COOH domain) from Escherichia coli.
true
true
true
true
true
1,039
3
INTRODUCTION
1
8
[ "B8", "B8" ]
17,617,643
pmid-16585763|pmid-16585763
We have used random and site-directed mutagenesis to map the functional domains of AraR required for DNA binding, dimerization and effector binding.
[ "8", "8" ]
148
6,316
0
false
We have used random and site-directed mutagenesis to map the functional domains of AraR required for DNA binding, dimerization and effector binding.
[]
We have used random and site-directed mutagenesis to map the functional domains of AraR required for DNA binding, dimerization and effector binding.
true
true
true
true
true
1,039
3
INTRODUCTION
1
8
[ "B8", "B8" ]
17,617,643
pmid-16585763|pmid-16585763
The arabinose-binding pocket is composed of polar and charged residues, whereas the dimerization interface has a hydrophobic nature.
[ "8", "8" ]
132
6,317
0
false
The arabinose-binding pocket is composed of polar and charged residues, whereas the dimerization interface has a hydrophobic nature.
[]
The arabinose-binding pocket is composed of polar and charged residues, whereas the dimerization interface has a hydrophobic nature.
true
true
true
true
true
1,039
3
INTRODUCTION
1
8
[ "B8", "B8" ]
17,617,643
pmid-16585763|pmid-16585763
In both cases, the residues are distributed along the primary sequence of the C-terminal domain (8).
[ "8", "8" ]
100
6,318
1
false
In both cases, the residues are distributed along the primary sequence of the C-terminal domain.
[ "8" ]
In both cases, the residues are distributed along the primary sequence of the C-terminal domain.
true
true
true
true
true
1,039
3
INTRODUCTION
1
8
[ "B8", "B8" ]
17,617,643
pmid-16585763|pmid-16585763
Based on crystallographic studies of structurally and functionally related proteins, binding of the effector to the COOH region in AraR is predicted to elicit a conformational change in the N-terminal region, leading to inhibition of binding to operator sequences, and allowing transcription from the arabinose-responsiv...
[ "8", "8" ]
332
6,319
0
false
Based on crystallographic studies of structurally and functionally related proteins, binding of the effector to the COOH region in AraR is predicted to elicit a conformational change in the N-terminal region, leading to inhibition of binding to operator sequences, and allowing transcription from the arabinose-responsiv...
[]
Based on crystallographic studies of structurally and functionally related proteins, binding of the effector to the COOH region in AraR is predicted to elicit a conformational change in the N-terminal region, leading to inhibition of binding to operator sequences, and allowing transcription from the arabinose-responsiv...
true
true
true
true
true
1,039
3
INTRODUCTION
1
8
[ "B8", "B8" ]
17,617,643
pmid-16585763|pmid-16585763
This allosteric signal involves a switching mechanism for communicating structural changes triggered in the sensor domain to the regulatory domain, decreasing the affinity of the latter for DNA.
[ "8", "8" ]
194
6,320
0
false
This allosteric signal involves a switching mechanism for communicating structural changes triggered in the sensor domain to the regulatory domain, decreasing the affinity of the latter for DNA.
[]
This allosteric signal involves a switching mechanism for communicating structural changes triggered in the sensor domain to the regulatory domain, decreasing the affinity of the latter for DNA.
true
true
true
true
true
1,039
4
INTRODUCTION
1
14
[ "B14", "B15", "B11", "B16", "B8" ]
17,617,643
pmid-8332212|pmid-10679470|pmid-11756427|pmid-12126620|pmid-16585763
Winged helix motifs are functionally and mechanistically versatile (14).
[ "14", "15", "11", "16", "8" ]
72
6,321
1
false
Winged helix motifs are functionally and mechanistically versatile.
[ "14" ]
Winged helix motifs are functionally and mechanistically versatile.
true
true
true
true
true
1,040
4
INTRODUCTION
1
14
[ "B14", "B15", "B11", "B16", "B8" ]
17,617,643
pmid-8332212|pmid-10679470|pmid-11756427|pmid-12126620|pmid-16585763
They are primarily involved in DNA binding, but cases have been reported in which they participate in protein–protein interactions.
[ "14", "15", "11", "16", "8" ]
131
6,322
0
false
They are primarily involved in DNA binding, but cases have been reported in which they participate in protein–protein interactions.
[]
They are primarily involved in DNA binding, but cases have been reported in which they participate in protein–protein interactions.
true
true
true
true
true
1,040
4
INTRODUCTION
1
15
[ "B14", "B15", "B11", "B16", "B8" ]
17,617,643
pmid-8332212|pmid-10679470|pmid-11756427|pmid-12126620|pmid-16585763
Monomeric, homo- or heterodimeric protein–DNA complexes have been characterized and revealed quite distinct modes of binding to DNA, which can involve interactions between the recognition helix and the wing with the major and minor groove (15).
[ "14", "15", "11", "16", "8" ]
244
6,323
1
false
Monomeric, homo- or heterodimeric protein–DNA complexes have been characterized and revealed quite distinct modes of binding to DNA, which can involve interactions between the recognition helix and the wing with the major and minor groove.
[ "15" ]
Monomeric, homo- or heterodimeric protein–DNA complexes have been characterized and revealed quite distinct modes of binding to DNA, which can involve interactions between the recognition helix and the wing with the major and minor groove.
true
true
true
true
true
1,040
4
INTRODUCTION
1
11
[ "B14", "B15", "B11", "B16", "B8" ]
17,617,643
pmid-8332212|pmid-10679470|pmid-11756427|pmid-12126620|pmid-16585763
Although the level of amino acid identity for the DBD of all members of the GntR superfamily is low (∼25%) they share this conserved structural topology (11).
[ "14", "15", "11", "16", "8" ]
158
6,324
1
false
Although the level of amino acid identity for the DBD of all members of the GntR superfamily is low (∼25%) they share this conserved structural topology.
[ "11" ]
Although the level of amino acid identity for the DBD of all members of the GntR superfamily is low (∼25%) they share this conserved structural topology.
true
true
true
true
true
1,040
4
INTRODUCTION
1
14
[ "B14", "B15", "B11", "B16", "B8" ]
17,617,643
pmid-8332212|pmid-10679470|pmid-11756427|pmid-12126620|pmid-16585763
Global analysis of the conservation of amino acid sequences in DNA-binding proteins concluded that residues interacting with the DNA backbone establish a set of core contacts that provide stability for homologous protein–DNA complexes, and consequently are well conserved across all protein families.
[ "14", "15", "11", "16", "8" ]
300
6,325
0
false
Global analysis of the conservation of amino acid sequences in DNA-binding proteins concluded that residues interacting with the DNA backbone establish a set of core contacts that provide stability for homologous protein–DNA complexes, and consequently are well conserved across all protein families.
[]
Global analysis of the conservation of amino acid sequences in DNA-binding proteins concluded that residues interacting with the DNA backbone establish a set of core contacts that provide stability for homologous protein–DNA complexes, and consequently are well conserved across all protein families.
true
true
true
true
true
1,040
4
INTRODUCTION
1
16
[ "B14", "B15", "B11", "B16", "B8" ]
17,617,643
pmid-8332212|pmid-10679470|pmid-11756427|pmid-12126620|pmid-16585763
On the other hand, residues that interact with DNA bases have more variable levels of conservation (16).
[ "14", "15", "11", "16", "8" ]
104
6,326
1
false
On the other hand, residues that interact with DNA bases have more variable levels of conservation.
[ "16" ]
On the other hand, residues that interact with DNA bases have more variable levels of conservation.
true
true
true
true
true
1,040
4
INTRODUCTION
1
8
[ "B14", "B15", "B11", "B16", "B8" ]
17,617,643
pmid-8332212|pmid-10679470|pmid-11756427|pmid-12126620|pmid-16585763
Previous mutagenic studies showed that AraR residues in the N-terminal region were required for DNA binding because mutations in these residues abolished its regulatory function in vivo (8).
[ "14", "15", "11", "16", "8" ]
190
6,327
1
false
Previous mutagenic studies showed that AraR residues in the N-terminal region were required for DNA binding because mutations in these residues abolished its regulatory function in vivo.
[ "8" ]
Previous mutagenic studies showed that AraR residues in the N-terminal region were required for DNA binding because mutations in these residues abolished its regulatory function in vivo.
true
true
true
true
true
1,040
4
INTRODUCTION
1
14
[ "B14", "B15", "B11", "B16", "B8" ]
17,617,643
pmid-8332212|pmid-10679470|pmid-11756427|pmid-12126620|pmid-16585763
However, the precise contribution of the mutated amino acids to DNA-binding activity was unclear.
[ "14", "15", "11", "16", "8" ]
97
6,328
0
false
However, the precise contribution of the mutated amino acids to DNA-binding activity was unclear.
[]
However, the precise contribution of the mutated amino acids to DNA-binding activity was unclear.
true
true
true
true
true
1,040
5
INTRODUCTION
0
null
null
17,617,643
null
To understand the specific properties of the interaction AraR-operator sequences, we substituted amino acids, in or near the HTH motif, which according to the model were predicted to contact DNA.
null
195
6,329
0
false
null
null
To understand the specific properties of the interaction AraR-operator sequences, we substituted amino acids, in or near the HTH motif, which according to the model were predicted to contact DNA.
true
true
true
true
true
1,041
5
INTRODUCTION
0
null
null
17,617,643
null
We determined the effects of these substitutions on the ability of AraR to function in vivo and on the DNA-binding affinities in vitro.
null
135
6,330
0
false
null
null
We determined the effects of these substitutions on the ability of AraR to function in vivo and on the DNA-binding affinities in vitro.
true
true
true
true
true
1,041
5
INTRODUCTION
0
null
null
17,617,643
null
Conversely, mutational analysis of the AraR-binding sites was used to determine the base-specific requirements for transcriptional regulation in vivo and DNA binding in vitro.
null
175
6,331
0
false
null
null
Conversely, mutational analysis of the AraR-binding sites was used to determine the base-specific requirements for transcriptional regulation in vivo and DNA binding in vitro.
true
true
true
true
true
1,041
5
INTRODUCTION
0
null
null
17,617,643
null
These experiments gave both expected and unexpected results, which together showed that specific AraR residues and operator bases are crucial to achieve a high level of regulatory activity, while others display variable contributions to DNA binding.
null
249
6,332
0
false
null
null
These experiments gave both expected and unexpected results, which together showed that specific AraR residues and operator bases are crucial to achieve a high level of regulatory activity, while others display variable contributions to DNA binding.
true
true
true
true
true
1,041
5
INTRODUCTION
0
null
null
17,617,643
null
In addition, an AraR mutant was isolated, which partially suppresses the loss of regulation observed in certain mutated DNA operators.
null
134
6,333
0
false
null
null
In addition, an AraR mutant was isolated, which partially suppresses the loss of regulation observed in certain mutated DNA operators.
true
true
true
true
true
1,041
0
INTRODUCTION
1
1
[ "b1", "b2" ]
17,145,710
pmid-14605208|pmid-14755292
The understanding of the cell machinery, the characterization of protein function as well as the discovery of new drug targets can be greatly enhanced by studying molecular interactions.
[ "1", "2" ]
186
6,334
0
false
The understanding of the cell machinery, the characterization of protein function as well as the discovery of new drug targets can be greatly enhanced by studying molecular interactions.
[]
The understanding of the cell machinery, the characterization of protein function as well as the discovery of new drug targets can be greatly enhanced by studying molecular interactions.
true
true
true
true
true
1,042
0
INTRODUCTION
1
1
[ "b1", "b2" ]
17,145,710
pmid-14605208|pmid-14755292
We have witnessed in the past few years, a considerable increase of the number of publications reporting molecular interaction, but also the amount of interactions reported in a single publication, scaling from a single to over 22 000 binary interactions (1).
[ "1", "2" ]
259
6,335
1
false
We have witnessed in the past few years, a considerable increase of the number of publications reporting molecular interaction, but also the amount of interactions reported in a single publication, scaling from a single to over 22 000 binary interactions.
[ "1" ]
We have witnessed in the past few years, a considerable increase of the number of publications reporting molecular interaction, but also the amount of interactions reported in a single publication, scaling from a single to over 22 000 binary interactions.
true
true
true
true
true
1,042
0
INTRODUCTION
1
1
[ "b1", "b2" ]
17,145,710
pmid-14605208|pmid-14755292
The fragmentation of the datasets as well as their lack of formal representation makes it often difficult to reuse the data as the foundation for further research.
[ "1", "2" ]
163
6,336
0
false
The fragmentation of the datasets as well as their lack of formal representation makes it often difficult to reuse the data as the foundation for further research.
[]
The fragmentation of the datasets as well as their lack of formal representation makes it often difficult to reuse the data as the foundation for further research.
true
true
true
true
true
1,042
0
INTRODUCTION
1
1
[ "b1", "b2" ]
17,145,710
pmid-14605208|pmid-14755292
IntAct addresses these issues by manually annotating published manuscripts reporting molecular interaction data and formalizing it by using a comprehensive set of controlled vocabularies in order to ensure data integrity.
[ "1", "2" ]
221
6,337
0
false
IntAct addresses these issues by manually annotating published manuscripts reporting molecular interaction data and formalizing it by using a comprehensive set of controlled vocabularies in order to ensure data integrity.
[]
IntAct addresses these issues by manually annotating published manuscripts reporting molecular interaction data and formalizing it by using a comprehensive set of controlled vocabularies in order to ensure data integrity.
true
true
true
true
true
1,042
0
INTRODUCTION
1
2
[ "b1", "b2" ]
17,145,710
pmid-14605208|pmid-14755292
The data are made publicly available using the PSI-MI XML Standard (2), providing end users with the highest level of details without compromising the integrity and simplicity of access to the data, thanks to the use of well established standards.
[ "1", "2" ]
247
6,338
1
false
The data are made publicly available using the PSI-MI XML Standard, providing end users with the highest level of details without compromising the integrity and simplicity of access to the data, thanks to the use of well established standards.
[ "2" ]
The data are made publicly available using the PSI-MI XML Standard, providing end users with the highest level of details without compromising the integrity and simplicity of access to the data, thanks to the use of well established standards.
true
true
true
true
true
1,042
0
DISCUSSION
0
null
null
17,145,710
pmid-14605208|pmid-14755292
IntAct has initially been developed to support local installation and has now instances running around the world.
null
113
6,339
0
false
null
null
IntAct has initially been developed to support local installation and has now instances running around the world.
true
true
true
true
true
1,043
0
DISCUSSION
0
null
null
17,145,710
pmid-14605208|pmid-14755292
Pharmaceutical companies, research laboratories as well as interaction databases have chosen to adopt our open source database and toolkit and whenever the need arise add novel or adapt existing functionality.
null
209
6,340
0
false
null
null
Pharmaceutical companies, research laboratories as well as interaction databases have chosen to adopt our open source database and toolkit and whenever the need arise add novel or adapt existing functionality.
true
true
true
true
true
1,043
0
DISCUSSION
0
null
null
17,145,710
pmid-14605208|pmid-14755292
If you are interested in a collaboration or a local IntAct installation, please contact us at intact-help@ebi.ac.uk or simply use the freely available source code.
null
163
6,341
0
false
null
null
If you are interested in a collaboration or a local IntAct installation, please contact us at intact-help@ebi.ac.uk or simply use the freely available source code.
true
true
true
true
true
1,043
1
DISCUSSION
1
14
[ "b14", "b15", "b16", "b17", "b18" ]
17,145,710
pmid-15608229|pmid-11911893|pmid-14681454|pmid-16381906|NA
Working toward giving fully inclusive access to the ever growing amount of molecular interaction data is a vast task, likely to be beyond the reach of any single interaction data resource.
[ "14", "15", "16", "17", "18" ]
188
6,342
0
false
Working toward giving fully inclusive access to the ever growing amount of molecular interaction data is a vast task, likely to be beyond the reach of any single interaction data resource.
[]
Working toward giving fully inclusive access to the ever growing amount of molecular interaction data is a vast task, likely to be beyond the reach of any single interaction data resource.
true
true
true
true
true
1,044
1
DISCUSSION
1
14
[ "b14", "b15", "b16", "b17", "b18" ]
17,145,710
pmid-15608229|pmid-11911893|pmid-14681454|pmid-16381906|NA
To share the curation workload, avoid redundant curation and ensure consistency in annotation policies, five public databases, BIND (14), MINT (15), DIP (16), MPact (17) and IntAct, have formed the IMEx consortium (IMEx—) to exchange molecular interaction records between partners.
[ "14", "15", "16", "17", "18" ]
281
6,343
1
false
To share the curation workload, avoid redundant curation and ensure consistency in annotation policies, five public databases, BIND, MINT, DIP, MPact and IntAct, have formed the IMEx consortium (IMEx—) to exchange molecular interaction records between partners.
[ "14", "15", "16", "17" ]
To share the curation workload, avoid redundant curation and ensure consistency in annotation policies, five public databases, BIND, MINT, DIP, MPact and IntAct, have formed the IMEx consortium (IMEx—) to exchange molecular interaction records between partners.
true
true
true
true
true
1,044
1
DISCUSSION
1
14
[ "b14", "b15", "b16", "b17", "b18" ]
17,145,710
pmid-15608229|pmid-11911893|pmid-14681454|pmid-16381906|NA
This cumulative effort should result in an overarching repository that is broader in scope and deeper in information than any individual efforts and one that scientists can use to better understand issues of health and disease or in the development of new drugs and therapeutics.
[ "14", "15", "16", "17", "18" ]
279
6,344
0
false
This cumulative effort should result in an overarching repository that is broader in scope and deeper in information than any individual efforts and one that scientists can use to better understand issues of health and disease or in the development of new drugs and therapeutics.
[]
This cumulative effort should result in an overarching repository that is broader in scope and deeper in information than any individual efforts and one that scientists can use to better understand issues of health and disease or in the development of new drugs and therapeutics.
true
true
true
true
true
1,044
1
DISCUSSION
1
14
[ "b14", "b15", "b16", "b17", "b18" ]
17,145,710
pmid-15608229|pmid-11911893|pmid-14681454|pmid-16381906|NA
To assist IMEx partners in capturing as much of published interaction data as possible, please refer to the IMEx website and submit your data pre-publication to one of the IMEx partners.
[ "14", "15", "16", "17", "18" ]
186
6,345
0
false
To assist IMEx partners in capturing as much of published interaction data as possible, please refer to the IMEx website and submit your data pre-publication to one of the IMEx partners.
[]
To assist IMEx partners in capturing as much of published interaction data as possible, please refer to the IMEx website and submit your data pre-publication to one of the IMEx partners.
true
true
true
true
true
1,044
1
DISCUSSION
1
18
[ "b14", "b15", "b16", "b17", "b18" ]
17,145,710
pmid-15608229|pmid-11911893|pmid-14681454|pmid-16381906|NA
To aid this process, and to ensure minimum data loss on submission due to the use of ambiguous or unstable identifiers, it is suggested that such data be compliant with the recently published Minimum Information required for reporting a Molecular Interaction Experiment (MIMIx) standard compliant (18).
[ "14", "15", "16", "17", "18" ]
302
6,346
1
false
To aid this process, and to ensure minimum data loss on submission due to the use of ambiguous or unstable identifiers, it is suggested that such data be compliant with the recently published Minimum Information required for reporting a Molecular Interaction Experiment (MIMIx) standard compliant.
[ "18" ]
To aid this process, and to ensure minimum data loss on submission due to the use of ambiguous or unstable identifiers, it is suggested that such data be compliant with the recently published Minimum Information required for reporting a Molecular Interaction Experiment (MIMIx) standard compliant.
true
true
true
true
true
1,044
0
INTRODUCTION
1
1
[ "B1", "B1 B2 B3", "B4", "B1", "B3", "B1", "B5 B6 B7 B8", "B8 B9 B10" ]
17,652,324
pmid-14988392|pmid-14988392|pmid-9846123|pmid-10966467|pmid-16185078|pmid-14988392|pmid-10966467|pmid-14988392|pmid-9440688|pmid-9857206|pmid-10364165|pmid-11389835|pmid-11389835|pmid-15035983|pmid-15210707
The high fidelity displayed by replicases from families A, B and C outcomes from 104 to 106-fold polymerase preference for inserting correct rather than incorrect nucleotides (1).
[ "1", "1–3", "4", "1", "3", "1", "5–8", "8–10" ]
179
6,347
1
false
The high fidelity displayed by replicases from families A, B and C outcomes from 104 to 106-fold polymerase preference for inserting correct rather than incorrect nucleotides.
[ "1" ]
The high fidelity displayed by replicases from families A, B and C outcomes from 104 to 106-fold polymerase preference for inserting correct rather than incorrect nucleotides.
true
true
true
true
true
1,045
0
INTRODUCTION
1
1–3
[ "B1", "B1 B2 B3", "B4", "B1", "B3", "B1", "B5 B6 B7 B8", "B8 B9 B10" ]
17,652,324
pmid-14988392|pmid-14988392|pmid-9846123|pmid-10966467|pmid-16185078|pmid-14988392|pmid-10966467|pmid-14988392|pmid-9440688|pmid-9857206|pmid-10364165|pmid-11389835|pmid-11389835|pmid-15035983|pmid-15210707
Such selectivity has traditionally been considered to rely on the base-pair shape and size, as the result of the geometric restraints imposed by the polymerase active site to tolerate equivalent Watson–Crick base pairs, ruling out those differing from this geometry (1–3).
[ "1", "1–3", "4", "1", "3", "1", "5–8", "8–10" ]
272
6,348
1
false
Such selectivity has traditionally been considered to rely on the base-pair shape and size, as the result of the geometric restraints imposed by the polymerase active site to tolerate equivalent Watson–Crick base pairs, ruling out those differing from this geometry.
[ "1–3" ]
Such selectivity has traditionally been considered to rely on the base-pair shape and size, as the result of the geometric restraints imposed by the polymerase active site to tolerate equivalent Watson–Crick base pairs, ruling out those differing from this geometry.
true
true
true
true
true
1,045
0
INTRODUCTION
1
4
[ "B1", "B1 B2 B3", "B4", "B1", "B3", "B1", "B5 B6 B7 B8", "B8 B9 B10" ]
17,652,324
pmid-14988392|pmid-14988392|pmid-9846123|pmid-10966467|pmid-16185078|pmid-14988392|pmid-10966467|pmid-14988392|pmid-9440688|pmid-9857206|pmid-10364165|pmid-11389835|pmid-11389835|pmid-15035983|pmid-15210707
Additionally, recent studies performed with non-natural nucleotides also suggest a role for the π–π stacking interactions between the aromatic rings of the incoming dNTP and amino acid residues for an efficient polymerization at least in family B DNA polymerases (4).
[ "1", "1–3", "4", "1", "3", "1", "5–8", "8–10" ]
267
6,349
1
false
Additionally, recent studies performed with non-natural nucleotides also suggest a role for the π–π stacking interactions between the aromatic rings of the incoming dNTP and amino acid residues for an efficient polymerization at least in family B DNA polymerases.
[ "4" ]
Additionally, recent studies performed with non-natural nucleotides also suggest a role for the π–π stacking interactions between the aromatic rings of the incoming dNTP and amino acid residues for an efficient polymerization at least in family B DNA polymerases.
true
true
true
true
true
1,045
0
INTRODUCTION
1
1
[ "B1", "B1 B2 B3", "B4", "B1", "B3", "B1", "B5 B6 B7 B8", "B8 B9 B10" ]
17,652,324
pmid-14988392|pmid-14988392|pmid-9846123|pmid-10966467|pmid-16185078|pmid-14988392|pmid-10966467|pmid-14988392|pmid-9440688|pmid-9857206|pmid-10364165|pmid-11389835|pmid-11389835|pmid-15035983|pmid-15210707
Polymerases contact DNA at positions in which both, topology and chemistry are identical among the four canonical base pairs.
[ "1", "1–3", "4", "1", "3", "1", "5–8", "8–10" ]
125
6,350
0
false
Polymerases contact DNA at positions in which both, topology and chemistry are identical among the four canonical base pairs.
[]
Polymerases contact DNA at positions in which both, topology and chemistry are identical among the four canonical base pairs.
true
true
true
true
true
1,045
0
INTRODUCTION
1
1
[ "B1", "B1 B2 B3", "B4", "B1", "B3", "B1", "B5 B6 B7 B8", "B8 B9 B10" ]
17,652,324
pmid-14988392|pmid-14988392|pmid-9846123|pmid-10966467|pmid-16185078|pmid-14988392|pmid-10966467|pmid-14988392|pmid-9440688|pmid-9857206|pmid-10364165|pmid-11389835|pmid-11389835|pmid-15035983|pmid-15210707
Thus, interactions occur mainly with the base, sugar and triphosphate moieties of the incoming nucleotide, with the nucleotide placed immediately 5′ with respect to the templating nucleotide and, most importantly, with the minor groove of the nascent base pair (1,3).
[ "1", "1–3", "4", "1", "3", "1", "5–8", "8–10" ]
267
6,351
0
false
Thus, interactions occur mainly with the base, sugar and triphosphate moieties of the incoming nucleotide, with the nucleotide placed immediately 5′ with respect to the templating nucleotide and, most importantly, with the minor groove of the nascent base pair.
[ "1,3" ]
Thus, interactions occur mainly with the base, sugar and triphosphate moieties of the incoming nucleotide, with the nucleotide placed immediately 5′ with respect to the templating nucleotide and, most importantly, with the minor groove of the nascent base pair.
true
true
true
true
true
1,045
0
INTRODUCTION
1
1
[ "B1", "B1 B2 B3", "B4", "B1", "B3", "B1", "B5 B6 B7 B8", "B8 B9 B10" ]
17,652,324
pmid-14988392|pmid-14988392|pmid-9846123|pmid-10966467|pmid-16185078|pmid-14988392|pmid-10966467|pmid-14988392|pmid-9440688|pmid-9857206|pmid-10364165|pmid-11389835|pmid-11389835|pmid-15035983|pmid-15210707
In this sense, structural studies of DNA polymerase complexes have revealed the presence of conserved residues at their catalytic sites that make contacts with the purine N3 and pyrimidine O2 atoms that act as hydrogen-bond acceptors and are positioned at similar locations in the minor groove (1,5–8).
[ "1", "1–3", "4", "1", "3", "1", "5–8", "8–10" ]
302
6,352
0
false
In this sense, structural studies of DNA polymerase complexes have revealed the presence of conserved residues at their catalytic sites that make contacts with the purine N3 and pyrimidine O2 atoms that act as hydrogen-bond acceptors and are positioned at similar locations in the minor groove.
[ "1,5–8" ]
In this sense, structural studies of DNA polymerase complexes have revealed the presence of conserved residues at their catalytic sites that make contacts with the purine N3 and pyrimidine O2 atoms that act as hydrogen-bond acceptors and are positioned at similar locations in the minor groove.
true
true
true
true
true
1,045
0
INTRODUCTION
1
1
[ "B1", "B1 B2 B3", "B4", "B1", "B3", "B1", "B5 B6 B7 B8", "B8 B9 B10" ]
17,652,324
pmid-14988392|pmid-14988392|pmid-9846123|pmid-10966467|pmid-16185078|pmid-14988392|pmid-10966467|pmid-14988392|pmid-9440688|pmid-9857206|pmid-10364165|pmid-11389835|pmid-11389835|pmid-15035983|pmid-15210707
Incorrect insertion of a nucleotide will move such H-acceptors out of position, breaking interactions with the polymerase and diminishing the DNA-binding stability at the polymerization site.
[ "1", "1–3", "4", "1", "3", "1", "5–8", "8–10" ]
191
6,353
0
false
Incorrect insertion of a nucleotide will move such H-acceptors out of position, breaking interactions with the polymerase and diminishing the DNA-binding stability at the polymerization site.
[]
Incorrect insertion of a nucleotide will move such H-acceptors out of position, breaking interactions with the polymerase and diminishing the DNA-binding stability at the polymerization site.
true
true
true
true
true
1,045
0
INTRODUCTION
1
8–10
[ "B1", "B1 B2 B3", "B4", "B1", "B3", "B1", "B5 B6 B7 B8", "B8 B9 B10" ]
17,652,324
pmid-14988392|pmid-14988392|pmid-9846123|pmid-10966467|pmid-16185078|pmid-14988392|pmid-10966467|pmid-14988392|pmid-9440688|pmid-9857206|pmid-10364165|pmid-11389835|pmid-11389835|pmid-15035983|pmid-15210707
This will result in an increased chance of the primer DNA to be switched to the 3′-5′ exonuclease site of the replicase to have the incorrect nucleotide removed (8–10).
[ "1", "1–3", "4", "1", "3", "1", "5–8", "8–10" ]
168
6,354
1
false
This will result in an increased chance of the primer DNA to be switched to the 3′-5′ exonuclease site of the replicase to have the incorrect nucleotide removed.
[ "8–10" ]
This will result in an increased chance of the primer DNA to be switched to the 3′-5′ exonuclease site of the replicase to have the incorrect nucleotide removed.
true
true
true
true
true
1,045
1
INTRODUCTION
1
11
[ "B11", "B12", "B13", "B14", "B15 B16 B17 B18 B19" ]
17,652,324
pmid-11357144|pmid-10688856|pmid-1992344|pmid-12483507|pmid-1991121|pmid-2027747|pmid-8068665|pmid-7846041|pmid-15297882
Lesions in the genomes arise by their continuous exposure to the action of toxic environmental agents such as ultraviolet and ionizing radiation, genotoxic chemicals, by-products of the normal metabolism like the reactive oxygen species (ROS), in addition to spontaneous breaks of chemical bonds (11).
[ "11", "12", "13", "14", "15–19" ]
301
6,355
1
false
Lesions in the genomes arise by their continuous exposure to the action of toxic environmental agents such as ultraviolet and ionizing radiation, genotoxic chemicals, by-products of the normal metabolism like the reactive oxygen species (ROS), in addition to spontaneous breaks of chemical bonds.
[ "11" ]
Lesions in the genomes arise by their continuous exposure to the action of toxic environmental agents such as ultraviolet and ionizing radiation, genotoxic chemicals, by-products of the normal metabolism like the reactive oxygen species (ROS), in addition to spontaneous breaks of chemical bonds.
true
true
true
true
true
1,046
1
INTRODUCTION
1
11
[ "B11", "B12", "B13", "B14", "B15 B16 B17 B18 B19" ]
17,652,324
pmid-11357144|pmid-10688856|pmid-1992344|pmid-12483507|pmid-1991121|pmid-2027747|pmid-8068665|pmid-7846041|pmid-15297882
Most organisms code for a number of enzymes to repair such damages before replication fork meeting them since replicative DNA polymerases stall when they come across one of these lesions as they cannot form a proper and catalytically competent ternary complex with the damaged nucleotide at their catalytic sites.
[ "11", "12", "13", "14", "15–19" ]
313
6,356
0
false
Most organisms code for a number of enzymes to repair such damages before replication fork meeting them since replicative DNA polymerases stall when they come across one of these lesions as they cannot form a proper and catalytically competent ternary complex with the damaged nucleotide at their catalytic sites.
[]
Most organisms code for a number of enzymes to repair such damages before replication fork meeting them since replicative DNA polymerases stall when they come across one of these lesions as they cannot form a proper and catalytically competent ternary complex with the damaged nucleotide at their catalytic sites.
true
true
true
true
true
1,046
1
INTRODUCTION
1
12
[ "B11", "B12", "B13", "B14", "B15 B16 B17 B18 B19" ]
17,652,324
pmid-11357144|pmid-10688856|pmid-1992344|pmid-12483507|pmid-1991121|pmid-2027747|pmid-8068665|pmid-7846041|pmid-15297882
One exception is the specially deleterious lesion 8-oxo-7,8,-dihydro-2′-deoxyguanosine (8oxodG), produced by ROS inside the cell (12) as, if it escapes the repair machinery, it can be used by the replicase as template or as incoming nucleotide.
[ "11", "12", "13", "14", "15–19" ]
244
6,357
1
false
One exception is the specially deleterious lesion 8-oxo-7,8,-dihydro-2′-deoxyguanosine (8oxodG), produced by ROS inside the cell as, if it escapes the repair machinery, it can be used by the replicase as template or as incoming nucleotide.
[ "12" ]
One exception is the specially deleterious lesion 8-oxo-7,8,-dihydro-2′-deoxyguanosine (8oxodG), produced by ROS inside the cell as, if it escapes the repair machinery, it can be used by the replicase as template or as incoming nucleotide.
true
true
true
true
true
1,046
1
INTRODUCTION
1
11
[ "B11", "B12", "B13", "B14", "B15 B16 B17 B18 B19" ]
17,652,324
pmid-11357144|pmid-10688856|pmid-1992344|pmid-12483507|pmid-1991121|pmid-2027747|pmid-8068665|pmid-7846041|pmid-15297882
The harmfulness of this lesion resides in its dual coding potential as it can pair with both cytosine and adenine during DNA synthesis, in the latter case leading to G to T transversions (13,14).
[ "11", "12", "13", "14", "15–19" ]
195
6,358
0
false
The harmfulness of this lesion resides in its dual coding potential as it can pair with both cytosine and adenine during DNA synthesis, in the latter case leading to G to T transversions.
[ "13,14" ]
The harmfulness of this lesion resides in its dual coding potential as it can pair with both cytosine and adenine during DNA synthesis, in the latter case leading to G to T transversions.
true
true
true
true
true
1,046
1
INTRODUCTION
1
15–19
[ "B11", "B12", "B13", "B14", "B15 B16 B17 B18 B19" ]
17,652,324
pmid-11357144|pmid-10688856|pmid-1992344|pmid-12483507|pmid-1991121|pmid-2027747|pmid-8068665|pmid-7846041|pmid-15297882
Structural studies of both 8oxodG:dC and 8oxodG:dA base pairs showed that 8oxodG adopts the classical anti conformation opposite dC, pairing in a Watson–Crick fashion, whereas its glycosidic bond adopts the syn orientation to form a Hoogsteen base pair with dA (15–19).
[ "11", "12", "13", "14", "15–19" ]
269
6,359
1
false
Structural studies of both 8oxodG:dC and 8oxodG:dA base pairs showed that 8oxodG adopts the classical anti conformation opposite dC, pairing in a Watson–Crick fashion, whereas its glycosidic bond adopts the syn orientation to form a Hoogsteen base pair with dA.
[ "15–19" ]
Structural studies of both 8oxodG:dC and 8oxodG:dA base pairs showed that 8oxodG adopts the classical anti conformation opposite dC, pairing in a Watson–Crick fashion, whereas its glycosidic bond adopts the syn orientation to form a Hoogsteen base pair with dA.
true
true
true
true
true
1,046
2
INTRODUCTION
1
19
[ "B19", "B20", "B19 B20 B21 B22 B23 B24", "B19" ]
17,652,324
pmid-15297882|pmid-15057282|pmid-15297882|pmid-15057282|pmid-9174365|pmid-9748338|pmid-11110788|pmid-16271888|pmid-15297882
Structural modelling of catalytically competent complexes of RB69 and T7 DNA polymerases have suggested that the preferential insertion of dC opposite such a lesion is accomplished by a handicapped dA incorporation since the O8 atom of the 8oxodG(syn):dA mispair sterically clashes with specific residues at the correspo...
[ "19", "20", "19–24", "19" ]
347
6,360
0
false
Structural modelling of catalytically competent complexes of RB69 and T7 DNA polymerases have suggested that the preferential insertion of dC opposite such a lesion is accomplished by a handicapped dA incorporation since the O8 atom of the 8oxodG(syn):dA mispair sterically clashes with specific residues at the correspo...
[ "19,20" ]
Structural modelling of catalytically competent complexes of RB69 and T7 DNA polymerases have suggested that the preferential insertion of dC opposite such a lesion is accomplished by a handicapped dA incorporation since the O8 atom of the 8oxodG(syn):dA mispair sterically clashes with specific residues at the correspo...
true
true
true
true
true
1,047
2
INTRODUCTION
1
19
[ "B19", "B20", "B19 B20 B21 B22 B23 B24", "B19" ]
17,652,324
pmid-15297882|pmid-15057282|pmid-15297882|pmid-15057282|pmid-9174365|pmid-9748338|pmid-11110788|pmid-16271888|pmid-15297882
However, notwithstanding their high insertion fidelity and preferential dC insertion during the bypass of 8oxodG-containing templates, replicases can misincorporate dA with a moderately high efficiency (19–24) due to the fact that such a base pair establishes appropriate hydrogen-bond interactions with the minor groove...
[ "19", "20", "19–24", "19" ]
365
6,361
1
false
However, notwithstanding their high insertion fidelity and preferential dC insertion during the bypass of 8oxodG-containing templates, replicases can misincorporate dA with a moderately high efficiency due to the fact that such a base pair establishes appropriate hydrogen-bond interactions with the minor groove sensing...
[ "19–24", "19" ]
However, notwithstanding their high insertion fidelity and preferential dC insertion during the bypass of 8oxodG-containing templates, replicases can misincorporate dA with a moderately high efficiency due to the fact that such a base pair establishes appropriate hydrogen-bond interactions with the minor groove sensing...
true
true
true
true
true
1,047
3
INTRODUCTION
1
25
[ "B25", "B26", "B27", "B28 B29 B30 B31", "B27" ]
17,652,324
pmid-8428945|pmid-1733957|pmid-2498321|pmid-3316215|pmid-9394619|pmid-1349852|pmid-3316214|pmid-2498321
Bacteriophage ϕ29 DNA polymerase is a protein-primed DNA-dependent replicase belonging to the eukaryotic-type family of DNA polymerases (family B).
[ "25", "26", "27", "28–31", "27" ]
147
6,362
0
false
Bacteriophage ϕ29 DNA polymerase is a protein-primed DNA-dependent replicase belonging to the eukaryotic-type family of DNA polymerases (family B).
[]
Bacteriophage ϕ29 DNA polymerase is a protein-primed DNA-dependent replicase belonging to the eukaryotic-type family of DNA polymerases (family B).
true
true
true
true
true
1,048
3
INTRODUCTION
1
25
[ "B25", "B26", "B27", "B28 B29 B30 B31", "B27" ]
17,652,324
pmid-8428945|pmid-1733957|pmid-2498321|pmid-3316215|pmid-9394619|pmid-1349852|pmid-3316214|pmid-2498321
Like many other replicases, it possesses, within a single polypeptide chain, both 5′–3′ polymerization and 3′–5′ exonuclease activities.
[ "25", "26", "27", "28–31", "27" ]
136
6,363
0
false
Like many other replicases, it possesses, within a single polypeptide chain, both 5′–3′ polymerization and 3′–5′ exonuclease activities.
[]
Like many other replicases, it possesses, within a single polypeptide chain, both 5′–3′ polymerization and 3′–5′ exonuclease activities.
true
true
true
true
true
1,048
3
INTRODUCTION
1
26
[ "B25", "B26", "B27", "B28 B29 B30 B31", "B27" ]
17,652,324
pmid-8428945|pmid-1733957|pmid-2498321|pmid-3316215|pmid-9394619|pmid-1349852|pmid-3316214|pmid-2498321
It displays a high intrinsic nucleotide insertion discrimination [104 to 106 (25)], which is further improved 100-fold through proofreading by the exonuclease domain (26).
[ "25", "26", "27", "28–31", "27" ]
171
6,364
1
false
It displays a high intrinsic nucleotide insertion discrimination, which is further improved 100-fold through proofreading by the exonuclease domain.
[ "104 to 106 (25)", "26" ]
It displays a high intrinsic nucleotide insertion discrimination, which is further improved 100-fold through proofreading by the exonuclease domain.
true
true
true
true
true
1,048
3
INTRODUCTION
1
25
[ "B25", "B26", "B27", "B28 B29 B30 B31", "B27" ]
17,652,324
pmid-8428945|pmid-1733957|pmid-2498321|pmid-3316215|pmid-9394619|pmid-1349852|pmid-3316214|pmid-2498321
ϕ29 DNA polymerase displays two unique characteristics compared with most replicases.
[ "25", "26", "27", "28–31", "27" ]
85
6,365
0
false
ϕ29 DNA polymerase displays two unique characteristics compared with most replicases.
[]
ϕ29 DNA polymerase displays two unique characteristics compared with most replicases.
false
true
true
true
false
1,048
3
INTRODUCTION
1
27
[ "B25", "B26", "B27", "B28 B29 B30 B31", "B27" ]
17,652,324
pmid-8428945|pmid-1733957|pmid-2498321|pmid-3316215|pmid-9394619|pmid-1349852|pmid-3316214|pmid-2498321
First, a DNA polymerase molecule replicates the entire genome processively without the assistance of processivity factors (27), in contrast to most replicases that require accessory proteins to clamp the enzyme to the DNA (28–31).
[ "25", "26", "27", "28–31", "27" ]
230
6,366
1
false
First, a DNA polymerase molecule replicates the entire genome processively without the assistance of processivity factors, in contrast to most replicases that require accessory proteins to clamp the enzyme to the DNA.
[ "27", "28–31" ]
First, a DNA polymerase molecule replicates the entire genome processively without the assistance of processivity factors, in contrast to most replicases that require accessory proteins to clamp the enzyme to the DNA.
true
true
true
true
true
1,048
3
INTRODUCTION
1
25
[ "B25", "B26", "B27", "B28 B29 B30 B31", "B27" ]
17,652,324
pmid-8428945|pmid-1733957|pmid-2498321|pmid-3316215|pmid-9394619|pmid-1349852|pmid-3316214|pmid-2498321
Second, ϕ29 DNA polymerase couples processive DNA polymerization to strand displacement.
[ "25", "26", "27", "28–31", "27" ]
88
6,367
0
false
Second, ϕ29 DNA polymerase couples processive DNA polymerization to strand displacement.
[]
Second, ϕ29 DNA polymerase couples processive DNA polymerization to strand displacement.
true
true
true
true
true
1,048
3
INTRODUCTION
1
27
[ "B25", "B26", "B27", "B28 B29 B30 B31", "B27" ]
17,652,324
pmid-8428945|pmid-1733957|pmid-2498321|pmid-3316215|pmid-9394619|pmid-1349852|pmid-3316214|pmid-2498321
This ability allows the enzyme to replicate the ϕ29 double-strand genome without the need for a helicase (27).
[ "25", "26", "27", "28–31", "27" ]
110
6,368
1
false
This ability allows the enzyme to replicate the ϕ29 double-strand genome without the need for a helicase.
[ "27" ]
This ability allows the enzyme to replicate the ϕ29 double-strand genome without the need for a helicase.
true
true
true
true
true
1,048
4
INTRODUCTION
1
32
[ "B32", "B33", "B34", "B35" ]
17,652,324
pmid-11959976|pmid-11381035|pmid-2055476|pmid-15546620
In this article, we study the ability of ϕ29 DNA polymerase to perform translesional synthesis past 8oxodG by assaying the nucleotide insertion opposite the lesion and further extension steps, as well as its capacity to proofread the formed pairs, this issue being of importance, as this enzyme is currently used for iso...
[ "32", "33", "34", "35" ]
396
6,369
0
false
In this article, we study the ability of ϕ29 DNA polymerase to perform translesional synthesis past 8oxodG by assaying the nucleotide insertion opposite the lesion and further extension steps, as well as its capacity to proofread the formed pairs, this issue being of importance, as this enzyme is currently used for iso...
[ "32,33" ]
In this article, we study the ability of ϕ29 DNA polymerase to perform translesional synthesis past 8oxodG by assaying the nucleotide insertion opposite the lesion and further extension steps, as well as its capacity to proofread the formed pairs, this issue being of importance, as this enzyme is currently used for iso...
true
true
true
true
true
1,049
4
INTRODUCTION
1
34
[ "B32", "B33", "B34", "B35" ]
17,652,324
pmid-11959976|pmid-11381035|pmid-2055476|pmid-15546620
Structural models mentioned above, together with multiple sequence alignments of DNA polymerases (34), as well as the availability of the crystallographic structure of ϕ29 DNA polymerase (35), have led us to analyse the role in translesional synthesis past 8oxodG of the invariant Tyr residue of the highly conserved B m...
[ "32", "33", "34", "35" ]
434
6,370
1
false
Structural models mentioned above, together with multiple sequence alignments of DNA polymerases, as well as the availability of the crystallographic structure of ϕ29 DNA polymerase, have led us to analyse the role in translesional synthesis past 8oxodG of the invariant Tyr residue of the highly conserved B motif of fa...
[ "34", "35" ]
Structural models mentioned above, together with multiple sequence alignments of DNA polymerases, as well as the availability of the crystallographic structure of ϕ29 DNA polymerase, have led us to analyse the role in translesional synthesis past 8oxodG of the invariant Tyr residue of the highly conserved B motif of fa...
true
true
true
true
true
1,049
4
INTRODUCTION
1
32
[ "B32", "B33", "B34", "B35" ]
17,652,324
pmid-11959976|pmid-11381035|pmid-2055476|pmid-15546620
The results obtained allow us to propose a principal and dual role for this residue as one of the key determinants that dictate nucleotide insertion and extension preferences during translesion synthesis past 8oxodG by family B replicases.
[ "32", "33", "34", "35" ]
239
6,371
0
false
The results obtained allow us to propose a principal and dual role for this residue as one of the key determinants that dictate nucleotide insertion and extension preferences during translesion synthesis past 8oxodG by family B replicases.
[]
The results obtained allow us to propose a principal and dual role for this residue as one of the key determinants that dictate nucleotide insertion and extension preferences during translesion synthesis past 8oxodG by family B replicases.
true
true
true
true
true
1,049
0
INTRODUCTION
1
1
[ "B1", "B2", "B3", "B4", "B5", "B6" ]
17,483,513
pmid-215319|NA|pmid-11106749|pmid-15659338|pmid-15931189|pmid-9841679
Protein synthesis is an essential activity that accounts for a large part of the ATP turnover in living cells.
[ "1", "2", "3", "4", "5", "6" ]
110
6,372
0
false
Protein synthesis is an essential activity that accounts for a large part of the ATP turnover in living cells.
[]
Protein synthesis is an essential activity that accounts for a large part of the ATP turnover in living cells.
true
true
true
true
true
1,050
0
INTRODUCTION
1
1
[ "B1", "B2", "B3", "B4", "B5", "B6" ]
17,483,513
pmid-215319|NA|pmid-11106749|pmid-15659338|pmid-15931189|pmid-9841679
This process is performed by large macromolecular machines composed of proteins and rRNA molecules.
[ "1", "2", "3", "4", "5", "6" ]
99
6,373
0
false
This process is performed by large macromolecular machines composed of proteins and rRNA molecules.
[]
This process is performed by large macromolecular machines composed of proteins and rRNA molecules.
true
true
true
true
true
1,050
0
INTRODUCTION
1
1
[ "B1", "B2", "B3", "B4", "B5", "B6" ]
17,483,513
pmid-215319|NA|pmid-11106749|pmid-15659338|pmid-15931189|pmid-9841679
These ribonucleoprotein complexes, called ribosomes, each comprise a small subunit and a large subunit that cooperate to decipher (translate) the information encoded in mRNA molecules.
[ "1", "2", "3", "4", "5", "6" ]
184
6,374
0
false
These ribonucleoprotein complexes, called ribosomes, each comprise a small subunit and a large subunit that cooperate to decipher (translate) the information encoded in mRNA molecules.
[]
These ribonucleoprotein complexes, called ribosomes, each comprise a small subunit and a large subunit that cooperate to decipher (translate) the information encoded in mRNA molecules.
true
true
true
true
true
1,050
0
INTRODUCTION
1
1
[ "B1", "B2", "B3", "B4", "B5", "B6" ]
17,483,513
pmid-215319|NA|pmid-11106749|pmid-15659338|pmid-15931189|pmid-9841679
Recruitment of the small (40S) eukaryotic ribosomal subunit onto a cellular mRNA generally occurs via the capped 5′end.
[ "1", "2", "3", "4", "5", "6" ]
119
6,375
0
false
Recruitment of the small eukaryotic ribosomal subunit onto a cellular mRNA generally occurs via the capped 5′end.
[ "40S" ]
Recruitment of the small eukaryotic ribosomal subunit onto a cellular mRNA generally occurs via the capped 5′end.
true
true
true
true
true
1,050
0
INTRODUCTION
1
1
[ "B1", "B2", "B3", "B4", "B5", "B6" ]
17,483,513
pmid-215319|NA|pmid-11106749|pmid-15659338|pmid-15931189|pmid-9841679
Since the AUG start codon of a gene can be located many hundreds (in some cases thousands) of nucleotides downstream of the 5′end, the 40S subunit then has to translocate (scan) along the mRNA to reach the initiation site (1).
[ "1", "2", "3", "4", "5", "6" ]
226
6,376
1
false
Since the AUG start codon of a gene can be located many hundreds (in some cases thousands) of nucleotides downstream of the 5′end, the 40S subunit then has to translocate (scan) along the mRNA to reach the initiation site.
[ "1" ]
Since the AUG start codon of a gene can be located many hundreds (in some cases thousands) of nucleotides downstream of the 5′end, the 40S subunit then has to translocate (scan) along the mRNA to reach the initiation site.
true
true
true
true
true
1,050
0
INTRODUCTION
1
1
[ "B1", "B2", "B3", "B4", "B5", "B6" ]
17,483,513
pmid-215319|NA|pmid-11106749|pmid-15659338|pmid-15931189|pmid-9841679
This processive, sequence-independent scanning phase involves at least 11 eukaryotic initiation factors [eIFs (2)], equivalent in Saccharomyces cerevisiae to at least 21 proteins, that participate in a series of different complexes, as well as a number of (largely undefined) conformational states.
[ "1", "2", "3", "4", "5", "6" ]
298
6,377
0
false
This processive, sequence-independent scanning phase involves at least 11 eukaryotic initiation factors, equivalent in Saccharomyces cerevisiae to at least 21 proteins, that participate in a series of different complexes, as well as a number of (largely undefined) conformational states.
[ "eIFs (2)" ]
This processive, sequence-independent scanning phase involves at least 11 eukaryotic initiation factors, equivalent in Saccharomyces cerevisiae to at least 21 proteins, that participate in a series of different complexes, as well as a number of (largely undefined) conformational states.
true
true
true
true
true
1,050
0
INTRODUCTION
1
3
[ "B1", "B2", "B3", "B4", "B5", "B6" ]
17,483,513
pmid-215319|NA|pmid-11106749|pmid-15659338|pmid-15931189|pmid-9841679
The control of translation initiation is a key determinant of growth, is important to the stress response (3) and, when malfunctional, contributes to disease states (4,5).
[ "1", "2", "3", "4", "5", "6" ]
171
6,378
1
false
The control of translation initiation is a key determinant of growth, is important to the stress response and, when malfunctional, contributes to disease states.
[ "3", "4,5" ]
The control of translation initiation is a key determinant of growth, is important to the stress response and, when malfunctional, contributes to disease states.
true
true
true
true
true
1,050
0
INTRODUCTION
1
1
[ "B1", "B2", "B3", "B4", "B5", "B6" ]
17,483,513
pmid-215319|NA|pmid-11106749|pmid-15659338|pmid-15931189|pmid-9841679
It is therefore important to understand rate control of this process at a quantitative level.
[ "1", "2", "3", "4", "5", "6" ]
93
6,379
0
false
It is therefore important to understand rate control of this process at a quantitative level.
[]
It is therefore important to understand rate control of this process at a quantitative level.
true
true
true
true
true
1,050
0
INTRODUCTION
1
6
[ "B1", "B2", "B3", "B4", "B5", "B6" ]
17,483,513
pmid-215319|NA|pmid-11106749|pmid-15659338|pmid-15931189|pmid-9841679
Moreover, as understanding of the molecular mechanisms underlying eIF function progresses, we will be able to fit them into a quantitative framework that can serve as a robust model for the overall process (6).
[ "1", "2", "3", "4", "5", "6" ]
210
6,380
1
false
Moreover, as understanding of the molecular mechanisms underlying eIF function progresses, we will be able to fit them into a quantitative framework that can serve as a robust model for the overall process.
[ "6" ]
Moreover, as understanding of the molecular mechanisms underlying eIF function progresses, we will be able to fit them into a quantitative framework that can serve as a robust model for the overall process.
true
true
true
true
true
1,050
1
INTRODUCTION
1
7
[ "B7", "B2", "B8", "B9", "B10", "B11", "B12", "B13", "B7", "B13 B14 B15", "B33" ]
17,483,513
pmid-10364246|NA|pmid-15164008|pmid-15240832|NA|pmid-9732867|pmid-15145951|pmid-11018020|pmid-10364246|pmid-11018020|pmid-11387228|pmid-12861028|pmid-11044999|pmid-9841679|pmid-12406227|pmid-2122455|pmid-14607835|pmid-9935150
Binding of the ternary complex (comprising Met-tRNAiMet, eIF2 and GTP) to the 40S subunit is stabilized by eIF1A and eIF3 (7) (Figure 1A).
[ "7", "2", "8", "9", "10", "11", "12", "13", "7", "13–15", "33" ]
138
6,381
1
false
Binding of the ternary complex to the 40S subunit is stabilized by eIF1A and eIF3 (Figure 1A).
[ "comprising Met-tRNAiMet, eIF2 and GTP", "7" ]
Binding of the ternary complex to the 40S subunit is stabilized by eIF1A and eIF3 (Figure 1A).
true
true
true
true
true
1,051
1
INTRODUCTION
1
2
[ "B7", "B2", "B8", "B9", "B10", "B11", "B12", "B13", "B7", "B13 B14 B15", "B33" ]
17,483,513
pmid-10364246|NA|pmid-15164008|pmid-15240832|NA|pmid-9732867|pmid-15145951|pmid-11018020|pmid-10364246|pmid-11018020|pmid-11387228|pmid-12861028|pmid-11044999|pmid-9841679|pmid-12406227|pmid-2122455|pmid-14607835|pmid-9935150
Yeast eIF3 binds to eIF2, thus promoting binding of mRNA to 40S; mammalian eIF3, on the other hand, seems to be capable of binding (in an RNA-dependent manner) directly to the 40S subunit (2).
[ "7", "2", "8", "9", "10", "11", "12", "13", "7", "13–15", "33" ]
192
6,382
1
false
Yeast eIF3 binds to eIF2, thus promoting binding of mRNA to 40S; mammalian eIF3, on the other hand, seems to be capable of binding (in an RNA-dependent manner) directly to the 40S subunit.
[ "2" ]
Yeast eIF3 binds to eIF2, thus promoting binding of mRNA to 40S; mammalian eIF3, on the other hand, seems to be capable of binding (in an RNA-dependent manner) directly to the 40S subunit.
true
true
true
true
true
1,051
1
INTRODUCTION
1
7
[ "B7", "B2", "B8", "B9", "B10", "B11", "B12", "B13", "B7", "B13 B14 B15", "B33" ]
17,483,513
pmid-10364246|NA|pmid-15164008|pmid-15240832|NA|pmid-9732867|pmid-15145951|pmid-11018020|pmid-10364246|pmid-11018020|pmid-11387228|pmid-12861028|pmid-11044999|pmid-9841679|pmid-12406227|pmid-2122455|pmid-14607835|pmid-9935150
eIF4F is anchored to the 5′end of the mRNA via the cap-binding protein eIF4E which, despite its small size, may play roles in a number of cellular processes (8,9).
[ "7", "2", "8", "9", "10", "11", "12", "13", "7", "13–15", "33" ]
163
6,383
0
false
eIF4F is anchored to the 5′end of the mRNA via the cap-binding protein eIF4E which, despite its small size, may play roles in a number of cellular processes.
[ "8,9" ]
eIF4F is anchored to the 5′end of the mRNA via the cap-binding protein eIF4E which, despite its small size, may play roles in a number of cellular processes.
false
true
true
true
false
1,051
1
INTRODUCTION
1
10
[ "B7", "B2", "B8", "B9", "B10", "B11", "B12", "B13", "B7", "B13 B14 B15", "B33" ]
17,483,513
pmid-10364246|NA|pmid-15164008|pmid-15240832|NA|pmid-9732867|pmid-15145951|pmid-11018020|pmid-10364246|pmid-11018020|pmid-11387228|pmid-12861028|pmid-11044999|pmid-9841679|pmid-12406227|pmid-2122455|pmid-14607835|pmid-9935150
Genetic experiments in yeast have indicated that eIF1, eIF2 and eIF5 influence start codon selection (10), while in vitro biochemical experiments have shown that eIF1 and eIF1A play roles in scanning and formation of the 48S complex, which comprises 40S, the eIFs and mRNA (11,12).
[ "7", "2", "8", "9", "10", "11", "12", "13", "7", "13–15", "33" ]
281
6,384
1
false
Genetic experiments in yeast have indicated that eIF1, eIF2 and eIF5 influence start codon selection, while in vitro biochemical experiments have shown that eIF1 and eIF1A play roles in scanning and formation of the 48S complex, which comprises 40S, the eIFs and mRNA.
[ "10", "11,12" ]
Genetic experiments in yeast have indicated that eIF1, eIF2 and eIF5 influence start codon selection, while in vitro biochemical experiments have shown that eIF1 and eIF1A play roles in scanning and formation of the 48S complex, which comprises 40S, the eIFs and mRNA.
true
true
true
true
true
1,051
1
INTRODUCTION
1
7
[ "B7", "B2", "B8", "B9", "B10", "B11", "B12", "B13", "B7", "B13 B14 B15", "B33" ]
17,483,513
pmid-10364246|NA|pmid-15164008|pmid-15240832|NA|pmid-9732867|pmid-15145951|pmid-11018020|pmid-10364246|pmid-11018020|pmid-11387228|pmid-12861028|pmid-11044999|pmid-9841679|pmid-12406227|pmid-2122455|pmid-14607835|pmid-9935150
A growing body of evidence indicates that, at least in budding yeast, eIF1, eIF2, eIF3 and eIF5 may bind to the 40S subunit as a preformed multifactor complex (MFC (13); Figure 1A).
[ "7", "2", "8", "9", "10", "11", "12", "13", "7", "13–15", "33" ]
181
6,385
0
false
A growing body of evidence indicates that, at least in budding yeast, eIF1, eIF2, eIF3 and eIF5 may bind to the 40S subunit as a preformed multifactor complex ; Figure 1A).
[ "MFC (13" ]
A growing body of evidence indicates that, at least in budding yeast, eIF1, eIF2, eIF3 and eIF5 may bind to the 40S subunit as a preformed multifactor complex ; Figure 1A).
true
true
true
true
true
1,051
1
INTRODUCTION
1
7
[ "B7", "B2", "B8", "B9", "B10", "B11", "B12", "B13", "B7", "B13 B14 B15", "B33" ]
17,483,513
pmid-10364246|NA|pmid-15164008|pmid-15240832|NA|pmid-9732867|pmid-15145951|pmid-11018020|pmid-10364246|pmid-11018020|pmid-11387228|pmid-12861028|pmid-11044999|pmid-9841679|pmid-12406227|pmid-2122455|pmid-14607835|pmid-9935150
Thus the MFC components, together with eIF1A, play a key role in 40S-mRNA recruitment, scanning of the 5′ untranslated region, and start codon recognition (7,13–15).
[ "7", "2", "8", "9", "10", "11", "12", "13", "7", "13–15", "33" ]
165
6,386
0
false
Thus the MFC components, together with eIF1A, play a key role in 40S-mRNA recruitment, scanning of the 5′ untranslated region, and start codon recognition.
[ "7,13–15" ]
Thus the MFC components, together with eIF1A, play a key role in 40S-mRNA recruitment, scanning of the 5′ untranslated region, and start codon recognition.
true
true
true
true
true
1,051
1
INTRODUCTION
1
7
[ "B7", "B2", "B8", "B9", "B10", "B11", "B12", "B13", "B7", "B13 B14 B15", "B33" ]
17,483,513
pmid-10364246|NA|pmid-15164008|pmid-15240832|NA|pmid-9732867|pmid-15145951|pmid-11018020|pmid-10364246|pmid-11018020|pmid-11387228|pmid-12861028|pmid-11044999|pmid-9841679|pmid-12406227|pmid-2122455|pmid-14607835|pmid-9935150
Recognition of the start codon in an mRNA leads to hydrolysis of eIF2-bound GTP, followed by 60S joining aided by eIF5B-GTP.
[ "7", "2", "8", "9", "10", "11", "12", "13", "7", "13–15", "33" ]
124
6,387
0
false
Recognition of the start codon in an mRNA leads to hydrolysis of eIF2-bound GTP, followed by 60S joining aided by eIF5B-GTP.
[]
Recognition of the start codon in an mRNA leads to hydrolysis of eIF2-bound GTP, followed by 60S joining aided by eIF5B-GTP.
true
true
true
true
true
1,051
1
INTRODUCTION
1
7
[ "B7", "B2", "B8", "B9", "B10", "B11", "B12", "B13", "B7", "B13 B14 B15", "B33" ]
17,483,513
pmid-10364246|NA|pmid-15164008|pmid-15240832|NA|pmid-9732867|pmid-15145951|pmid-11018020|pmid-10364246|pmid-11018020|pmid-11387228|pmid-12861028|pmid-11044999|pmid-9841679|pmid-12406227|pmid-2122455|pmid-14607835|pmid-9935150
Hydrolysis of the latter GTP precedes initiation of protein synthesis.
[ "7", "2", "8", "9", "10", "11", "12", "13", "7", "13–15", "33" ]
70
6,388
0
false
Hydrolysis of the latter GTP precedes initiation of protein synthesis.
[]
Hydrolysis of the latter GTP precedes initiation of protein synthesis.
true
true
true
true
true
1,051
1
INTRODUCTION
1
7
[ "B7", "B2", "B8", "B9", "B10", "B11", "B12", "B13", "B7", "B13 B14 B15", "B33" ]
17,483,513
pmid-10364246|NA|pmid-15164008|pmid-15240832|NA|pmid-9732867|pmid-15145951|pmid-11018020|pmid-10364246|pmid-11018020|pmid-11387228|pmid-12861028|pmid-11044999|pmid-9841679|pmid-12406227|pmid-2122455|pmid-14607835|pmid-9935150
Figure 1.Construction and characterization of strains (see genotypes in Table 2) with doxycycline-regulatable eIF genes.
[ "7", "2", "8", "9", "10", "11", "12", "13", "7", "13–15", "33" ]
120
6,389
0
false
Figure 1.Construction and characterization of strains with doxycycline-regulatable eIF genes.
[ "see genotypes in Table 2" ]
Figure 1.Construction and characterization of strains with doxycycline-regulatable eIF genes.
true
true
true
true
true
1,051
1
INTRODUCTION
1
7
[ "B7", "B2", "B8", "B9", "B10", "B11", "B12", "B13", "B7", "B13 B14 B15", "B33" ]
17,483,513
pmid-10364246|NA|pmid-15164008|pmid-15240832|NA|pmid-9732867|pmid-15145951|pmid-11018020|pmid-10364246|pmid-11018020|pmid-11387228|pmid-12861028|pmid-11044999|pmid-9841679|pmid-12406227|pmid-2122455|pmid-14607835|pmid-9935150
(A) Eukaryotic translation initiation pathway, highlighting involvement of eIF4E, eIF4G, eIF1A and eIF5B in the phases of 40S recruitment [1], scanning and AUG recognition
[ "7", "2", "8", "9", "10", "11", "12", "13", "7", "13–15", "33" ]
171
6,390
0
false
(A) Eukaryotic translation initiation pathway, highlighting involvement of eIF4E, eIF4G, eIF1A and eIF5B in the phases of 40S recruitment [1], scanning and AUG recognition
[]
(A) Eukaryotic translation initiation pathway, highlighting involvement of eIF4E, eIF4G, eIF1A and eIF5B in the phases of 40S recruitment [1], scanning and AUG recognition
false
false
false
true
false
1,051
1
INTRODUCTION
1
2
[ "B7", "B2", "B8", "B9", "B10", "B11", "B12", "B13", "B7", "B13 B14 B15", "B33" ]
17,483,513
pmid-10364246|NA|pmid-15164008|pmid-15240832|NA|pmid-9732867|pmid-15145951|pmid-11018020|pmid-10364246|pmid-11018020|pmid-11387228|pmid-12861028|pmid-11044999|pmid-9841679|pmid-12406227|pmid-2122455|pmid-14607835|pmid-9935150
[2] and subunit joining [3].
[ "7", "2", "8", "9", "10", "11", "12", "13", "7", "13–15", "33" ]
28
6,391
1
false
and subunit joining [3].
[ "2" ]
and subunit joining [3].
false
true
true
true
false
1,051
1
INTRODUCTION
1
7
[ "B7", "B2", "B8", "B9", "B10", "B11", "B12", "B13", "B7", "B13 B14 B15", "B33" ]
17,483,513
pmid-10364246|NA|pmid-15164008|pmid-15240832|NA|pmid-9732867|pmid-15145951|pmid-11018020|pmid-10364246|pmid-11018020|pmid-11387228|pmid-12861028|pmid-11044999|pmid-9841679|pmid-12406227|pmid-2122455|pmid-14607835|pmid-9935150
(B) Strategy for promoter substitution upstream of eIF-encoding genes.
[ "7", "2", "8", "9", "10", "11", "12", "13", "7", "13–15", "33" ]
70
6,392
0
false
(B) Strategy for promoter substitution upstream of eIF-encoding genes.
[]
(B) Strategy for promoter substitution upstream of eIF-encoding genes.
false
false
true
true
false
1,051
1
INTRODUCTION
1
33
[ "B7", "B2", "B8", "B9", "B10", "B11", "B12", "B13", "B7", "B13 B14 B15", "B33" ]
17,483,513
pmid-10364246|NA|pmid-15164008|pmid-15240832|NA|pmid-9732867|pmid-15145951|pmid-11018020|pmid-10364246|pmid-11018020|pmid-11387228|pmid-12861028|pmid-11044999|pmid-9841679|pmid-12406227|pmid-2122455|pmid-14607835|pmid-9935150
The tetO7 promoter (33) was inserted between 50 and 200 bp upstream of each ORF.
[ "7", "2", "8", "9", "10", "11", "12", "13", "7", "13–15", "33" ]
80
6,393
1
false
The tetO7 promoter was inserted between 50 and 200 bp upstream of each ORF.
[ "33" ]
The tetO7 promoter was inserted between 50 and 200 bp upstream of each ORF.
true
true
true
true
true
1,051
1
INTRODUCTION
1
7
[ "B7", "B2", "B8", "B9", "B10", "B11", "B12", "B13", "B7", "B13 B14 B15", "B33" ]
17,483,513
pmid-10364246|NA|pmid-15164008|pmid-15240832|NA|pmid-9732867|pmid-15145951|pmid-11018020|pmid-10364246|pmid-11018020|pmid-11387228|pmid-12861028|pmid-11044999|pmid-9841679|pmid-12406227|pmid-2122455|pmid-14607835|pmid-9935150
(C) Complementation of doxycycline (2 μg ml−1) -induced growth phenotypes was tested on SGal-uracil plates [YCp33Supex2-CDC33 (YCp-CDC33) and YCp33Supex2-TIF4631 (YCp-TIF4631)], or on SD-uracil plates [pRS316-TIF11 (pRS-TIF11) and pRS316-FUN12 (pRS-FUN12)].
[ "7", "2", "8", "9", "10", "11", "12", "13", "7", "13–15", "33" ]
257
6,394
0
false
(C) Complementation of doxycycline -induced growth phenotypes was tested on SGal-uracil plates, or on SD-uracil plates.
[ "2 μg ml−1", "YCp33Supex2-CDC33 (YCp-CDC33) and YCp33Supex2-TIF4631 (YCp-TIF4631)", "pRS316-TIF11 (pRS-TIF11) and pRS316-FUN12 (pRS-FUN12)" ]
(C) Complementation of doxycycline -induced growth phenotypes was tested on SGal-uracil plates, or on SD-uracil plates.
false
false
true
true
false
1,051
2
INTRODUCTION
1
33
[ "B33" ]
17,483,513
pmid-11044999
Construction and characterization of strains (see genotypes in Table 2) with doxycycline-regulatable eIF genes.
[ "33" ]
111
6,395
0
false
Construction and characterization of strains (see genotypes in Table 2) with doxycycline-regulatable eIF genes.
[]
Construction and characterization of strains (see genotypes in Table 2) with doxycycline-regulatable eIF genes.
true
true
true
true
true
1,052
2
INTRODUCTION
1
33
[ "B33" ]
17,483,513
pmid-11044999
(A) Eukaryotic translation initiation pathway, highlighting involvement of eIF4E, eIF4G, eIF1A and eIF5B in the phases of 40S recruitment [1], scanning and AUG recognition
[ "33" ]
171
6,396
0
false
(A) Eukaryotic translation initiation pathway, highlighting involvement of eIF4E, eIF4G, eIF1A and eIF5B in the phases of 40S recruitment [1], scanning and AUG recognition
[]
(A) Eukaryotic translation initiation pathway, highlighting involvement of eIF4E, eIF4G, eIF1A and eIF5B in the phases of 40S recruitment [1], scanning and AUG recognition
false
false
false
true
false
1,052
2
INTRODUCTION
1
33
[ "B33" ]
17,483,513
pmid-11044999
[2] and subunit joining [3].
[ "33" ]
28
6,397
0
false
[2] and subunit joining [3].
[]
[2] and subunit joining.
false
false
true
true
false
1,052
2
INTRODUCTION
1
33
[ "B33" ]
17,483,513
pmid-11044999
(B) Strategy for promoter substitution upstream of eIF-encoding genes.
[ "33" ]
70
6,398
0
false
(B) Strategy for promoter substitution upstream of eIF-encoding genes.
[]
(B) Strategy for promoter substitution upstream of eIF-encoding genes.
false
false
true
true
false
1,052
2
INTRODUCTION
1
33
[ "B33" ]
17,483,513
pmid-11044999
The tetO7 promoter (33) was inserted between 50 and 200 bp upstream of each ORF.
[ "33" ]
80
6,399
1
false
The tetO7 promoter was inserted between 50 and 200 bp upstream of each ORF.
[ "33" ]
The tetO7 promoter was inserted between 50 and 200 bp upstream of each ORF.
true
true
true
true
true
1,052